Project ID: plumID:24.000
Source: scripts/LAMMPS/plumed_LAMMPS/plumed.dat
Originally used with PLUMED version: 2.8.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTARTUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
H:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=1,2,3the numerical indexes for the set of atoms in the group
N:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=4,5,6the numerical indexes for the set of atoms in the group
Li:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=7,8,9the numerical indexes for the set of atoms in the group
ghosta:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=0,0,15coordinates of the virtual atom
max_nn:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=Nthis keyword is used for colvars such as the coordination numberSPECIESB=Nthis keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=1.6 D_MAX=5}the switching function that it used in the construction of the contact matrixMAX={BETA=0.01} #max_nn_focus: COORDINATIONNUMBER SPECIESA=$ATOM1 SPECIESB=$ATOM2 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01} max_nn_focus:calculate the maximum valueCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=4this keyword is used for colvars such as the coordination numberSPECIESB=1this keyword is used for colvars such as the coordination numberSWITCH={RATIONAL R_0=1.6 D_MAX=5}the switching function that it used in the construction of the contact matrixMAX={BETA=0.01} d1:calculate the maximum valueDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,4 #$ATOM1,$ATOM2the pair of atom that we are calculating the distance between
dis_GH:ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. More detailsGROUPA=ghostaCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=HCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.5} uwall1:calculate the maximum valueUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dis_GH.maxthe arguments on which the bias is actingAT=12.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2 dis_GN:the powers for the wallsZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. More detailsGROUPA=ghostaCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=NCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.5} uwall2:calculate the maximum valueUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dis_GN.maxthe arguments on which the bias is actingAT=12.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsOPES_METAD...On-the-fly probability enhanced sampling with metadynamics-like target distribution. More detailsLABEL=opes2a label for the action so that its output can be referenced in the input to other actionsARG=max_nn.maxthe input for this action is the scalar output from one or more other actionsPACE=250the frequency for kernel depositionBARRIER=200the free energy barrier to be overcomeTEMP=750 #RESTART=NOtemperatureFILE=Kernels_Bb200.data.data #STATE_RFILE=Restart_Bb200.dataa file in which the list of all deposited kernels is storedSTATE_WFILE=State_Bb200.datawrite to this file the compressed kernels and all the info needed to RESTART the simulationSTATE_WSTRIDE=2000number of MD steps between writing the STATE_WFILESIGMA_MIN=0.001never reduce SIGMA below this valueSTORE_STATES... OPES_METADappend to STATE_WFILE instead of ovewriting it each timePrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=400the frequency with which the quantities of interest should be outputFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=400the frequency with which all the open files should be flushed